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- PDB-3i69: Apo Glutathione Transferase A1-1 GIMF-helix mutant -

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Basic information

Entry
Database: PDB / ID: 3i69
TitleApo Glutathione Transferase A1-1 GIMF-helix mutant
ComponentsGlutathione S-transferase A1
KeywordsTRANSFERASE / human GST A1-1 / enzyme
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process ...Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / glutathione metabolic process / epithelial cell differentiation / xenobiotic metabolic process / fatty acid binding / extracellular exosome / cytosol
Similarity search - Function
Glutathione S-transferase, alpha class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase, alpha class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutathione S-transferase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / isomorphous to another structure / Resolution: 2.38 Å
AuthorsBalogh, L.M. / Le Trong, I. / Stenkamp, R.E. / Atkins, W.M.
CitationJournal: Biochemistry / Year: 2009
Title: Structural analysis of a glutathione transferase A1-1 mutant tailored for high catalytic efficiency with toxic alkenals.
Authors: Balogh, L.M. / Le Trong, I. / Kripps, K.A. / Tars, K. / Stenkamp, R.E. / Mannervik, B. / Atkins, W.M.
History
DepositionJul 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2011Group: Non-polymer description
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase A1
B: Glutathione S-transferase A1
C: Glutathione S-transferase A1
D: Glutathione S-transferase A1
E: Glutathione S-transferase A1
F: Glutathione S-transferase A1
G: Glutathione S-transferase A1
H: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,24010
Polymers205,6258
Non-polymers6152
Water4,306239
1
A: Glutathione S-transferase A1
B: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7143
Polymers51,4062
Non-polymers3071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-20 kcal/mol
Surface area20730 Å2
MethodPISA
2
C: Glutathione S-transferase A1
D: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7143
Polymers51,4062
Non-polymers3071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-23 kcal/mol
Surface area20390 Å2
MethodPISA
3
E: Glutathione S-transferase A1
F: Glutathione S-transferase A1


Theoretical massNumber of molelcules
Total (without water)51,4062
Polymers51,4062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-23 kcal/mol
Surface area20750 Å2
MethodPISA
4
G: Glutathione S-transferase A1
H: Glutathione S-transferase A1


Theoretical massNumber of molelcules
Total (without water)51,4062
Polymers51,4062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-22 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.896, 114.684, 97.538
Angle α, β, γ (deg.)90.00, 117.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutathione S-transferase A1 / / GTH1 / HA subunit 1 / GST-epsilon / GSTA1-1 / GST class-alpha member 1


Mass: 25703.109 Da / Num. of mol.: 8
Mutation: A12G, L107I, L108M, V111F, M208P, K211I, S212Y, L213V, E214R, E215T, A216V, R217Y, K218N, F222P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P08263, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% PEG 4000, 0.1 M Tric-Cl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 15, 2008
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 83015 / Num. obs: 83015 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.75 / Num. unique all: 7933 / % possible all: 94.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
structurefactor calculator for an isomorphous structuremodel building
REFMAC5.5.0047refinement
HKL-2000data reduction
HKL-2000data scaling
structurefactor calculator for an isomorphous structurephasing
RefinementMethod to determine structure: isomorphous to another structure
Resolution: 2.38→47.22 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.888 / SU B: 12.788 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.573 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.289 3752 5 %RANDOM
Rwork0.225 ---
all0.228 75117 --
obs0.228 71365 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.363 Å2
Baniso -1Baniso -2Baniso -3
1-6.04 Å20 Å22.08 Å2
2---3.15 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.38→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14241 0 40 239 14520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02214616
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210483
X-RAY DIFFRACTIONr_angle_refined_deg1.1562.00319689
X-RAY DIFFRACTIONr_angle_other_deg0.845325618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72251743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06923.941642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.611152806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.561590
X-RAY DIFFRACTIONr_chiral_restr0.060.22150
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022882
X-RAY DIFFRACTIONr_mcbond_it0.8932.58767
X-RAY DIFFRACTIONr_mcbond_other0.1582.53477
X-RAY DIFFRACTIONr_mcangle_it1.5883.7514198
X-RAY DIFFRACTIONr_scbond_it1.59545849
X-RAY DIFFRACTIONr_scangle_it2.45865491
LS refinement shellResolution: 2.38→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 266 -
Rwork0.332 5187 -
obs--98.55 %

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